Showing : GenomicRanges • reset
1
vote
1
reply
1.3k
views
How to make combined annotation of 5'UTRs and CDS's?
annotation concatenation GRangesList GenomicRanges
6.6 years ago anmej • 0
0
votes
2
replies
1.2k
views
feel confused when identifying overlapping regions by intersect method
GenomicRanges overlaps intersect
updated 6.7 years ago by ★ 11k • written 6.7 years ago by • 0
2
votes
1
reply
1.8k
views
Create a matrix to show overlaps among multiple GRanges
r GRanges GenomicRanges
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 40
6
votes
8
replies
3.9k
views
Ranges from a fasta file
biostrings fasta genomicranges granges
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 90
6
votes
12
replies
2.9k
views
mclapply to loop over a GRangesList object
GenomicRanges GRanges GRangesList parallel mclapply
6.7 years ago foehn ▴ 100
0
votes
4
replies
2.4k
views
Unexpected behaviour of set operations on GRanges objects when dplyr is loaded
GenomicRanges S4Vectors dplyr
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 140
2
votes
2
replies
2.8k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 6.8 years ago by ★ 29k • written 6.8 years ago by • 0
4
votes
2
replies
1.5k
views
Speed efficient way to select the n-th element from GRangsList
R GenomicRanges IRanges
6.9 years ago foehn ▴ 100
0
votes
1
reply
1.1k
views
How is it possible to override the constructor of the GRanges class?
genomicranges granges
6.9 years ago Shaurya Jauhari • 0
5
votes
8
replies
11k
views
Non overlapping granges (or opposite of subsetByOverlaps)
granges genomicranges iranges subsetByOverlaps
updated 3.7 years ago by • 0 • written 10.1 years ago by ▴ 50
0
votes
1
reply
1.6k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.9 years ago by ★ 11k • written 6.9 years ago by • 0
2
votes
1
reply
1.5k
views
Bug in follow and precede
software error genomicranges iranges
updated 6.9 years ago by ★ 6.8k • written 6.9 years ago by • 0
1
vote
2
replies
3.6k
views
How to convert bedgraph to wig
rtracklayer genomicranges
updated 6.9 years ago by ★ 11k • written 6.9 years ago by • 0
0
votes
7
replies
1.8k
views
rtracklayer cannot export empty BED file
rtracklayer bed genomicranges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 100
1
vote
1
reply
924
views
Bug report for GenomicRanges
genomicranges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ▴ 170
7
votes
5
replies
4.9k
views
summarize scores of GRanges into bins
genomicranges grangeslist bin findoverlaps
updated 7.0 years ago by • 0 • written 8.1 years ago by ★ 1.5k
0
votes
1
reply
842
views
How to find overlaps in genomic sequences comparing patients to themselves
genomicranges
7.0 years ago sbailey5 • 0
0
votes
2
replies
1.4k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
7.0 years ago A ▴ 60
0
votes
3
replies
1.6k
views
GenomicRanges based on indices or more conditions, and add column from match
genomicranges iranges findoverlaps
7.1 years ago francesca casalino ▴ 50
2
votes
1
reply
1.4k
views
Intra-range transformation on GPos-objects?
genomicranges gpos granges
updated 7.1 years ago by 16k • written 7.1 years ago by ▴ 180
0
votes
0
replies
1.8k
views
GenomicFeatures: How to extract a gene's upstream region of TSS up to the end position of the flanking (nearby) gene.
genomicranges genomicfeatures promoter upstream_flank
7.1 years ago Wojeff • 0
2
votes
2
replies
5.1k
views
Concatenate a list of genomic ranges
r granges genomicranges
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
2
replies
994
views
Error: the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
genomicranges
7.2 years ago bbrink • 0
3
votes
3
replies
1.8k
views
Gaia results including negative widths
gaia genomicranges iranges
updated 7.2 years ago by ▴ 40 • written 7.2 years ago by ▴ 10
1
vote
1
reply
3.1k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.3 years ago by ▴ 20 • written 7.3 years ago by • 0
0
votes
3
replies
1.4k
views
Nearest genomic ranges and distances in circular ranges
genomicranges
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by • 0
0
votes
3
replies
1.0k
views
'downstream' disappeared from GenomicRanges package?
genomicranges
7.3 years ago Vang Le ▴ 80
3
votes
2
replies
1.4k
views
Simplifying a RaggedExperiment using qreduceAssay and weighted means.
raggedexperiment genomicranges
updated 7.3 years ago by 25k • written 7.3 years ago by ★ 1.1k
5
votes
4
replies
2.7k
views
How do I do a bedtools like intersection in GenomicRanges?
genomicranges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 40
2
votes
12
replies
2.7k
views
nearest without overlapping
genomicranges
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 40
1
vote
5
replies
3.5k
views
Replacement for lapply on a GRanges?
genomicranges
updated 7.4 years ago by 16k • written 7.4 years ago by ▴ 890
7
votes
5
replies
2.6k
views
Strange error in bsseq when trying to assign seqinfo
bsseq genomeinfodb genomicranges seqinfo
written 7.5 years ago by ▴ 140
0
votes
1
reply
1.5k
views
GenomicRanges distanceToNearest: trouble replicating snp-gene mapping from older version
GenomicRanges distancetonearest strandedness
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by • 0
0
votes
1
reply
1.3k
views
Detect Sites with Minimum Gap in GRanges Object
R genomicranges granges grange
7.6 years ago g.k • 0
2
votes
2
replies
1.2k
views
Features within 2kb window, but with resampling
genomicranges granges slidingwindow
updated 7.6 years ago by ★ 11k • written 7.6 years ago by • 0
3
votes
1
reply
1.0k
views
Finding the nearest n genes from a genomic loci
genomicranges
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 20
1
vote
2
replies
1.6k
views
extending GenomicRanges::reduce warning, why ?
GenomicRanges reduce setMethod setGeneric
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 80
1
vote
3
replies
2.1k
views
How to operate on circular sequences with GenomicRanges?
GenomicRanges mitochondria circular
updated 7.7 years ago by ★ 6.8k • written 7.7 years ago by ▴ 120
3
votes
2
replies
2.5k
views
coverage() output SimpleRleList cannot be converted to GRanges
bug genomicranges granges rlelist coverage
updated 7.7 years ago by 16k • written 7.7 years ago by ▴ 10
0
votes
5
replies
1.4k
views
Problem converting annotation to GenomicRanges object
genomicranges
7.7 years ago Anton01 • 0
3
votes
4
replies
1.7k
views
Future plans for the new GPos class
genomicranges gpos
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 180
2
votes
8
replies
6.5k
views
GenomicRanges: identify overlapping regions, get intersection between each overlapping pair and add gene coordinates (start, end, strand and ids)
genomicranges overlap intersect findoverlaps
7.8 years ago Caroline Grisbach Meissner ▴ 10
2
votes
3
replies
1.9k
views
GRanges object from gene list
granges bed genomicranges genomeintervals deseq2
7.8 years ago rbronste ▴ 60
2
votes
4
replies
2.1k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 7.8 years ago by ★ 11k • written 7.8 years ago by ▴ 20
0
votes
0
replies
1.1k
views
coverage no longer works on GPos objects?
genomicranges gpos
7.8 years ago maltethodberg ▴ 180
1
vote
4
replies
4.4k
views
Generate 3' UTR and 5' UTR ranges from a gff file
gff genomicranges
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 10
0
votes
6
replies
4.7k
views
GRanges::distanceToNearest does not return distance to nearest
granges genomicranges
updated 7.9 years ago by ★ 6.8k • written 7.9 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Error when subsetting a RaggedExperiment by GenomicRanges
raggedexperiment genomicranges
updated 7.9 years ago by 700 • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
GenomicRanges fails to load due to missing ngap method
software error genomicranges loadnamespace
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
0
votes
2
replies
1.2k
views
GRangesList: wiered error
genomicranges genomicfeatures
7.9 years ago Fabian Grammes ▴ 20
403 results • Page 3 of 9
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Hervé Pagès 16k
Popular Question to Ou, Jianhong ★ 1.3k
Popular Question to Maria Doyle ▴ 100
Popular Question to Gordon Smyth 53k
Locations • All
United States, 1 hour ago
The city by the bay, 1 hour ago
United States, 5 hours ago
Barcelona, Spain, 7 hours ago
United States, 8 hours ago
Traffic: 641 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6